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PubMed2002

The Bioperl toolkit: Perl modules for the life sciences.

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.

Algorithms↗
PubMed1995

bioTk:componentry for genome informatics graphical user interfaces.

bioTk is a collection of graphical "widgets" and utilities that support application programming in the domain of bioinformatics. It is intended to establish a framework that encourages the development of communicating window-based applications and flexible, non-modal user interaction. The current release of bioTk has domain-specific widgets for chromosome ideogram displays, genome maps, and scrolling sequence windows.

Base Sequence↗
PubMed1991

Collaborations in art/science: Renaissance teams.

A Renaissance Team is a group of specialists who collaborate and provide synergism in the quest for knowledge and information. Artists can participate in Renaissance Teams with scientists and computer specialists for scientific visualization projects. Some projects are described in which the author functioned as programmer and color expert, as interface designer, as visual paradigm maker, as animator, and as producer. Examples are provided for each of these five projects.

Art↗
PubMed1978

Management data for collection analysis and development.

Sound management data are needed to evaluate the collections of health sciences libraries. This study reports the utilization of computer data bases to compare the libary collections of The University of Texas Health Science Center at San Antonio. The University of Texas Medical Branch, and the National Library of Medicine's CATLINE data base. The imprint dates of the records of two libraries are compared to measure acquisitions rates. Subject profiles for the Q and W classes demonstrate the similarity of the collections. Reasons for the variances are considered.

Analysis of Variance↗
PubMed2005

The impact of computing technology on pharmaceutical and biotech research.

Pharmaceutical and biotechnology companies continue to make investments in research techniques including those using high-performance computing technology. Much of this research is fueled by the need to analyze the ever-growing store of genomic and proteomic data. However, many research and development investments, including techniques to mine newly produced genomic data, have not provided the anticipated improvements in productivity. This raises the questions of whether advancements expected from next-generation computing technology can translate into tangible benefits for pharmaceutical and biotechnology researchers, and whether researchers can capitalize on an increased understanding of biological systems using tools made more readily available in high-performance computing. The author provides some background on the source of the advancements in the computing industry and offers examples from other scientific applications that point to potential benefits in life science research.

Biotechnology↗
PubMed2005

Audiovisual touch-screen computer-assisted self-interviewing for donor health histories: results from two years experience with the system.

BACKGROUND: The donor history interview is an important aspect of blood safety, in part designed to identify unsuitable donors who may present a risk to blood recipients. There is evidence from behavioral science literature that use of computer-assisted interviewing may be superior to face-to-face (FTF) and paper techniques in eliciting sensitive behavioral information of interest to blood collection facilities. STUDY DESIGN AND METHODS: Audiovisual touch-screen computer-assisted donor self-interviewing with the AABB Uniform Donor History Questionnaire was deployed for routine use in a regional blood center replacing FTF interviews. Donor and staff perception and satisfaction surveys were performed to assess acceptance of the system. Time studies of automated and manual methods were conducted. Rates of deferral of first-time donors for high-risk behaviors and rates of errors and omissions on donor interviewing for the two systems were tabulated and compared. RESULTS: Donors and staff strongly preferred the automated system in all dimensions assessed. Donor time increased by 4 minutes but staff time declined by 5 minutes per interview. Identification of high-risk behaviors among first-time donors significantly increased. Rates of errors and omissions on donor history forms identified at audit were reduced. CONCLUSIONS: Both blood donors and collections staff enthusiastically accepted the automated donor interviewing system. A well-designed audiovisual touch-screen donor self-interviewing system is superior to face-to-face interviewing and most likely more effective than paper interviewing.

Attitude of Health Personnel↗
PubMed2002

Introduction to the special issue on virtual reality environments in behavioral sciences.

Virtual reality (VR) is usually described in biology and in medicine as a collection of technologies that allow people to interact efficiently with three-dimensional (3-D) computerized databases in real time using their natural senses. This definition lacks any reference to head-mounted displays (HMDs) and instrumented clothing such as gloves or suits. In fact, less than 10% of VR healthcare applications in medicine are actually using any immersive equipment. However, if we focus our attention on behavioral sciences, where immersion is used by more than 50% of the applications, VR is described as an advanced form of human- computer interface that allows the user to interact with and become immersed in a computer-generated environment. This difference outlines a different vision of VR shared by psychologists, psychotherapists, and neuropsychologists: VR provides a new human-computer interaction paradigm in which users are no longer simply external observers of images on a computer screen but are active participants within a computer-generated 3-D virtual world. This special issue investigates this vision, presenting some of the most interesting applications actually developed in the area. Moreover, it discusses the clinical principles, human factors, and technological issues associated with the use of VR in the behavioral sciences.

Behavioral Sciences↗
PubMedDate not supplied

X-ray diffraction computed tomography.

Coherent scattering of x-ray photons leads to the phenomenon of x-ray diffraction, which is widely used for determining atomic structure in materials science. A technique [x-ray diffraction computed tomography (CT)] is described, analogous to conventional CT, in which the x-ray diffraction properties of a stack of two-dimensional object sections may be imaged. The technique has been investigated using a first generation (single pencil beam) CT scanner to measure small angle coherent scatter, in addition to the customary transmitted radiation. Diffraction data from a standard CT performance phantom obtained with this new technique and with an x-ray diffractometer are compared. The agreement is satisfactory bearing in mind the poor momentum resolution of our apparatus. The dose and sensitivity of x-ray diffraction CT are compared with those of conventional transmission CT. Diffraction patterns of some biological tissues and plastics presented in a companion paper indicate the potential of x-ray diffraction CT for tissue discrimination and material characterization. Finally, possibilities for refinement of the technique by improving the momentum resolution are discussed.

Computers↗
PubMed1998

Evaluating polynomials on the molecular level--a novel approach to molecular computers.

In the past few years two fascinating and new scientific fields, the science of DNA-structure and topology and the theory of molecular computers have been growing independently. The main goal of this paper is to establish an interesting connection between them and to propose a novel paradigm for the future construction of DNA-computing devices based on supercoil energetics. The basic principle of the proposed model can also be applied to describe the communication between topologically closed segments in real genomes, which is believed to take part in the complex process of gene regulation. An implementation of the recent model is proposed by which polynomials of one real variable can be evaluated in a simple in vitro recombination assay.

Computers↗
PubMed1994

Global information infrastructure.

The High Performance Computing and Communications Program (HPCC) is a multiagency federal initiative under the leadership of the White House Office of Science and Technology Policy, established by the High Performance Computing Act of 1991. It has been assigned a critical role in supporting the international collaboration essential to science and to health care. Goals of the HPCC are to extend USA leadership in high performance computing and networking technologies; to improve technology transfer for economic competitiveness, education, and national security; and to provide a key part of the foundation for the National Information Infrastructure. The first component of the National Institutes of Health to participate in the HPCC, the National Library of Medicine (NLM), recently issued a solicitation for proposals to address a range of issues, from privacy to 'testbed' networks, 'virtual reality,' and more. These efforts will build upon the NLM's extensive outreach program and other initiatives, including the Unified Medical Language System (UMLS), MEDLARS, and Grateful Med. New Internet search tools are emerging, such as Gopher and 'Knowbots'. Medicine will succeed in developing future intelligent agents to assist in utilizing computer networks. Our ability to serve patients is so often restricted by lack of information and knowledge at the time and place of medical decision-making. The new technologies, properly employed, will also greatly enhance our ability to serve the patient.

Computer Communication Networks↗
PubMed2001

Steric Turnoff of Vibrationally Mediated Negative Differential Resistance in a Single Molecule This work was supported by the National Science Foundation (DMR-9417866) and by the Cornell Center for Materials Research (CCMR), a Materials Research and Engineering Center of the National Science Foundation (DMR-9632275). Particular acknowledgement is made of the use of the Computing and Materials Facilities of the CCMR.

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Journal Article↗
PubMedDate not supplied

Computers in respiratory therapy education.

Microcomputers are widely available in schools of respiratory therapy and in hospital respiratory therapy departments and are influencing this and other areas of health science education in a major way. Computer-assisted instruction is a versatile, efficient means of providing content expertise in both settings.

Computer-Assisted Instruction↗
PubMed2004

Improved dissection efficiency in the human gross anatomy laboratory by the integration of computers and modern technology.

The need to increase the efficiency of dissection in the gross anatomy laboratory has been the driving force behind the technologic changes we have recently implemented. With the introduction of an integrated systems-based medical curriculum and a reduction in laboratory teaching hours, anatomy faculty at the University of North Texas Health Science Center (UNTHSC) developed a computer-based dissection manual to adjust to these curricular changes and time constraints. At each cadaver workstation, Apple iMac computers were added and a new dissection manual, running in a browser-based format, was installed. Within the text of the manual, anatomical structures required for dissection were linked to digital images from prosected materials; in addition, for each body system, the dissection manual included images from cross sections, radiographs, CT scans, and histology. Although we have placed a high priority on computerization of the anatomy laboratory, we remain strong advocates of the importance of cadaver dissection. It is our belief that the utilization of computers for dissection is a natural evolution of technology and fosters creative teaching strategies adapted for anatomy laboratories in the 21st century. Our strategy has significantly enhanced the independence and proficiency of our students, the efficiency of their dissection time, and the quality of laboratory instruction by the faculty.

Anatomy↗
PubMed1996

Tree and loop as moments for measurement.

Biologically motivated computing presents us with a measurement process in science. It triggers an epistemological shift from state-oriented physics to measurement-oriented physics, in which we can find a parallelism with Wittgenstein's shift from rule following to a language game. We argue here that an approximation or computing process can be viewed as a language game and propose an idea of proto-computing which is metaphorically formalized through disequilibration between tree- and loop-program, as a model for measurement-oriented computing.

Computer Simulation↗